Owner

VEuPathDB

37 indexed repositories · View on GitHub

ApiCommonWebsite

Perl · 3 stars
EbrcWebsiteCommon

Perl · 3 stars
web-monorepo
A monorepo that contains all frontend code for VEuPathDB websites

TypeScript · 3 stars
MicrobiomeWebsite

R · 2 stars
ClinEpiWebsite

CSS · 2 stars
ClinEpiModel

Java · 1 star
EbrcModelCommon

Java · 1 star
repeat-masker-nextflow
nextflow workflow to modernize current repeatMasker workflow steps

Perl · 1 star
dnaseq-nextflow
DNASeq Alignments with SNP and CNV nextflow workflow

Julia · 1 star
ApiCommonModel

Perl · 1 star
lib-compute-platform
Async compute platform core.

Kotlin · 1 star
WDK

Java · 1 star
SiteSearchData
WDK Model and other code needed to run a WDK and generate reports to make JSON files to index in solr

Python · 1 star
ApiCommonWorkflow

Perl · 1 star
lib-eda-subsetting
Provides Java interface to query and provide EDA data and metadata from a database

Java · 0 stars
tool-eda-file-dumper

Java · 0 stars
service-eda
Repo containing EDA web service

Java · 0 stars
service-sequence-retrieval
REST service for sequence retrieval , reads subsequences from FASTA files using `htsjdk`

Java · 0 stars
ApiCommonWebService

Java · 0 stars
antismash-nextflow

Perl · 0 stars
17 more repositories live on View on GitHub

Beginner friendly Everything

Open All

Add new improved strain calling algorithm to plasmoFAST Open

VEuPathDB/web-monorepo#1887 · 1 assignee · Opened Sep 19, 2026
Make genomics project dependency lists data-driven instead of hand-copied Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

VEuPathDB/ApiCommonWorkflow#107 · Opened Sep 14, 2026
MCP admission lane failed Open

mcp-conformance

Difficulty 3/5 1-2 days Newbie friendliness 48/100

VEuPathDB/pathfinder-app#2 · Opened Sep 12, 2026
Move regular dependency `diff` to devDependencies in genomics package.json Open

bug technical debt

VEuPathDB/web-monorepo#1880 · 1 assignee · Opened Sep 7, 2026
Bug: new Genetic Variation gene page sections don't expand/collapse properly Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 65/100

VEuPathDB/web-monorepo#1878 · Opened Sep 7, 2026
WDK nightly lane failed Open

wdk-drift

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

VEuPathDB/pathfinder-app#1 · 3 comments · Opened Sep 7, 2026
Replace `experimentalOrganism` individual object field with organism details list field. Open

internals rest api

VEuPathDB/vdi-service#717 · 1 assignee · Opened Sep 4, 2026
Apollo release: emit update commands only where Apollo's stored fields differ Open

Difficulty 3/5 1-2 days Newbie friendliness 76/100

VEuPathDB/ApiCommonModel#229 · Opened Aug 26, 2026
"All" pathway semantics behave as "any": HAVING compares a per-gene group count to a total row count Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

VEuPathDB/ApiCommonModel#228 · Opened Aug 25, 2026
Apollo release: updateCommand does not refresh commonName on an annotation-version bump Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

VEuPathDB/ApiCommonModel#225 · Opened Aug 24, 2026
Minor: Organism Presets layout is skewy in Revise Step modal Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

VEuPathDB/web-monorepo#1866 · Opened Aug 24, 2026
DE notebook - timepoint overlay is discrete, grouping is continuous and binned Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 45/100

VEuPathDB/web-monorepo#1865 · Opened Aug 21, 2026
Make EDA service human and agent-friendly through discoverability Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

VEuPathDB/service-eda#169 · 1 comment · Opened Aug 20, 2026
Switch Variant WDK elements from includeProjects to excludeProjects Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

VEuPathDB/ApiCommonModel#221 · Opened Aug 17, 2026
Minor: browser tab title should not be default 'project' when opening `user-comments/ai-gene-publication/add` in a new tab Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

VEuPathDB/web-monorepo#1853 · Opened Aug 17, 2026
Revisit EdaDatasetGraph outputEntity handling Open

technical debt

Difficulty 4/5 3-5 days Newbie friendliness 35/100

VEuPathDB/web-monorepo#1851 · Opened Aug 13, 2026
in a component site the installer should ignore genes that belong to other projects. Open

VEuPathDB/vdi-plugin-genelist#64 · 1 assignee · Opened Aug 12, 2026
rnaseqrc is ignoring the reference genome. Open

bug

VEuPathDB/vdi-plugin-wrangler#93 · 1 assignee · Opened Aug 11, 2026
WGCNA search - don't show modules irrelevant to the site Open

bug

VEuPathDB/web-monorepo#1844 · 1 comment · 1 assignee · Opened Aug 11, 2026
user-datasets depends on jquery without declaring it Open

technical debt

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

VEuPathDB/web-monorepo#1840 · Opened Aug 8, 2026
user-datasets: polling does not abort in-flight requests on teardown Open

technical debt

Difficulty 4/5 3-5 days Newbie friendliness 58/100

VEuPathDB/web-monorepo#1839 · Opened Aug 8, 2026
mergeExperiments output is not reproducible across runs (CANN slot order, avg_percent rounding) Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 48/100

VEuPathDB/dnaseq-nextflow#27 · Opened Aug 3, 2026
CANN: reference-allele slot of a multiallelic record can inherit r0, reporting the reference amino acid for a strain whose product is unknown Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

VEuPathDB/dnaseq-nextflow#26 · Opened Jul 31, 2026
MapVEu - supporting plots OutputEntityCount has no count Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

VEuPathDB/web-monorepo#1831 · Opened Jul 31, 2026
MapVEu supporting plots - boxplot allows longitude erroneously as x-axis variable Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 55/100

VEuPathDB/web-monorepo#1830 · Opened Jul 31, 2026
Plugin ignores `type.version` from `vdi-meta.json` Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

VEuPathDB/vdi-plugin-wrangler#89 · Opened Jul 29, 2026
AI-assisted gene comments - minor tweaks list Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

VEuPathDB/ApiCommonWebsite#306 · Opened Jul 23, 2026
dataExplorer: Update Metadata -> immediately close shouldn't trigger a page update Open

Difficulty 3/5 1-2 days Newbie friendliness 67/100

VEuPathDB/web-monorepo#1814 · Opened Jul 22, 2026
dataExplorer Datasets menu can be empty when My Datasets is collapsed by default? Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

VEuPathDB/web-monorepo#1813 · 1 comment · Opened Jul 22, 2026
Fix long-broken `updateMarkers`/`geohash` animation tests in `@veupathdb/components` Open

technical debt

Difficulty 3/5 1-2 days Newbie friendliness 68/100

VEuPathDB/web-monorepo#1804 · Opened Jul 16, 2026
`entity_from_file` should handle completely empty lines in the input file Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 68/100

VEuPathDB/study-wrangler#88 · Opened Jul 15, 2026
formatting issue with certain characters in the attributes file Open

bug

VEuPathDB/web-monorepo#1794 · 1 assignee · Opened Jul 9, 2026
Figure out EDA-based downloads Open

bug

Difficulty 5/5 Over a week Newbie friendliness 35/100

VEuPathDB/web-monorepo#1785 · Opened Jul 8, 2026
OrthoMCL: phyletic search taxonomic tree does not highlight with the current search when revising Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

VEuPathDB/web-monorepo#1781 · Opened Jul 8, 2026
Add EDA validation to forbid integer categorical variables Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

VEuPathDB/study-wrangler#82 · Opened Jun 17, 2026
Error handling or fix it: after a site rebuild i am a guest and my user datasets page throws an error Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

VEuPathDB/web-monorepo#1759 · 3 comments · Opened Jun 12, 2026
Error handling: make a meaningful one: when a guest or diff user tries to access a user dataset from other Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

VEuPathDB/web-monorepo#1758 · Opened Jun 12, 2026
Create public dataset validation JSON schema for genomics. Open

admin

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

VEuPathDB/vdi-service#678 · Opened Jun 10, 2026
User Dataset Upload Form: malformed help link Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

VEuPathDB/web-monorepo#1734 · 1 comment · Opened Jun 4, 2026
User dataset upload form (and beyond): tame the red in the user-datasets upload form Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 68/100

VEuPathDB/web-monorepo#1729 · Opened Jun 3, 2026
dataset properties install lane Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

VEuPathDB/vdi-service#668 · Opened May 29, 2026
Gene-publication AI-assisted user-comments phase 1b and 2 improvements Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

VEuPathDB/web-monorepo#1686 · Opened May 13, 2026
gene page Transcript Expression table Proposal: don't open the first item automatically Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

VEuPathDB/web-monorepo#1684 · 1 comment · Opened May 12, 2026
Notebook subsetting table filter <Enter> press submits form/reloads page Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 64/100

VEuPathDB/web-monorepo#1681 · Opened May 11, 2026
Strategy step revise: (Rapidly) pressing <enter> in strategy revise numeric boxes submits form with pre-edited value Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

VEuPathDB/web-monorepo#1680 · Opened May 8, 2026
processSequenceVariations.jl: VCF cache output should retain multi-allelic records Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

VEuPathDB/dnaseq-nextflow#10 · Opened May 6, 2026
Check binWidth calculations on single-value columns and fix if needed Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 52/100

VEuPathDB/study-wrangler#76 · Opened Apr 28, 2026
Map suitability detection for EDA studies should check that there are actually lat/long values, via metadata only: Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

VEuPathDB/web-monorepo#1677 · 1 comment · Opened Apr 28, 2026
Cleanup: A slew of console errors and warnings! Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

VEuPathDB/web-monorepo#1672 · 1 comment · Opened Apr 21, 2026
Add app db CRUD operations for datasetSources values. Open

app db internals

VEuPathDB/vdi-service#641 · 1 assignee · Opened Apr 15, 2026

Showing the newest 100

This page lists what was indexed most recently. Advanced filter has the whole inventory, narrowed by language, difficulty and how long a task takes.

Open advanced filter

VEuPathDB

Showing the newest 100

Get new issues in your inbox